I just received my stainless steel D&D dice. They look great but have what look like large grains wedged in some of the spaces. Is there a technique for getting these out or is it just the nature of the system.

Also is it safe to assume the SS is waterproof? I do plan on using these in D&D...

Yes, this is a real PITA!
What you are seeing on/in your parts is actually a specially treated, ground corn cob . It produces the final high shine on all SS parts. The finishing machinery generates a high pressure tumbling action and there is no way around having some cob residue finding it's way into tight crevices. There is no "solvent" for this that would not also attack the metal (in a bad way) in fact any liquid will make things worse because the cob expands when wet. Try a #10 Exacto blade, better than a needle or dental pick.
-G

"Where the spirit does not work with the hand, there is no art."
Leonardo da Vinci